It seems that this story would have eventually taken the film to LV-426, the planet from Alien and Aliens, thus finally and fully connecting these prequels to the original franchise.
Alien: Covenant screenwriter John Logan either has or would have wrote the script for the sequel, tentatively titled Alien: Awakening.
According to Empire (via HNE), John Logan’s script may have dealt with the Engineers that survived the genocide coming after David for revenge.